For the most part, income from personal services is sourced where the work is being done - for you, that's Kansas. There are a handful of exceptions in states that have a convenience of the employer rule. Virginia is not one of those states, so in your case, all of your income would be Kansas source.
Your employer erroneously withheld state tax for Virginia when they should be withholding state tax for Kansas, since you don't actually have any Virginia sourced income. Them simply being incorporated in Virginia doesn't make your income Virginia source. Unfortunately, we see this a lot at tax time and it can be confusing for taxpayers.
Since they did withhold the tax in Virginia, you're correct that you need to file a nonresident return to get a refund of the tax withholding. Because you didn't physically work in Virginia, you would indicate that $0 of your income is Virginia sourced as @MaryK4 mentioned above. This should zero out your Virginia return and show all of your tax withholding as a refund.
You will need to pay tax to Kansas on this income since there hasn't been any tax withholding. Going forward, you can request that they stop withholding Virginia tax from your pay and instead withhold Kansas. If they refuse to withhold tax for Kansas, I recommend making estimated tax payments to Kansas to avoid having a balance due on your tax return.
